3. First steps with Junifer

Note

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flowchart TD start((( Start ))) read_understanding(Read Understanding Junifer) start --> read_understanding question_features{Can I compute\nthe features I want\nusing junifer?} read_understanding --> question_features question_features -->|Yes| read_using_final question_features -->|I'm not sure| read_using question_features -->|No| question_feature_type read_using --> question_features read_using(Read Using Junifer) question_feature_type{"What am I missing\nfrom junifer"} question_feature_type --> missing_datagrabber question_feature_type --> missing_preprocessing question_feature_type --> missing_marker question_feature_type --> missing_other missing_datagrabber("A Dataset/DataGrabber") missing_preprocessing("A Preprocessing") missing_marker("A Marker") missing_other("Something else") missing_datagrabber --> question_datagrabber_junifarm question_datagrabber_junifarm{Is the\ndataset/datagrabber\nin juni-farm?} question_datagrabber_junifarm -->|Yes| read_using_final question_datagrabber_junifarm -->|No| read_extending_datagrabber_start read_extending_datagrabber_start(Read Creating a Junifer extension) read_extending_datagrabber_start --> read_extending_datagrabber read_extending_datagrabber(Read Creating Data Grabbers) read_extending_datagrabber --> question_datagrabber_kind question_datagrabber_kind{Is your dataset\na datalad one?} question_datagrabber_kind -->|Yes| extend_datagrabber_datalad question_datagrabber_kind -->|No| extend_datagrabber_pattern extend_datagrabber_pattern(Use\nPatternDataGrabber) extend_datagrabber_datalad(Use\nPatternDataladDataGrabber) extend_datagrabber_pattern --> question_datagrabber_solved extend_datagrabber_datalad --> question_datagrabber_solved question_datagrabber_solved{Can you use\nyour data now?} question_datagrabber_solved -->|Yes| question_contribute_datagrabber question_datagrabber_solved -->|No| contact_help question_contribute_datagrabber{Do you think\nyour DataGrabber\nis useful for other users?} question_contribute_datagrabber -->|Yes| contribute_datagrabber question_contribute_datagrabber -->|No| final_run contribute_datagrabber(Create a\nDATASET REQUEST\nissue on Github) contribute_datagrabber --> final_run missing_marker --> question_marker_junifarm question_marker_junifarm{Is the marker\nin juni-farm?} question_marker_junifarm -->|Yes| read_using_final question_marker_junifarm -->|No| read_extending_marker_start read_extending_marker_start(Read Creating a Junifer extension) read_extending_marker_start --> read_extending_marker read_extending_marker(Read Creating Markers) read_extending_marker --> question_marker_solved question_marker_solved{Can you use\nyour marker now?} question_marker_solved -->|Yes| question_contribute_marker question_marker_solved -->|No| contact_help question_contribute_marker{Do you think\nyour Marker\nis useful for other users?} question_contribute_marker -->|Yes| contribute_marker question_contribute_marker -->|No| final_run contribute_marker(Create a\nMARKER REQUEST\nissue on Github) contribute_marker --> final_run missing_preprocessing --> contact_help missing_mask{"A Mask?"} missing_parcellation{"A Parcellation?"} missing_coordinates{"Coordinates?"} missing_other_other{"Something else?"} missing_other --> missing_mask missing_other --> missing_parcellation missing_other --> missing_coordinates missing_other --> missing_other_other missing_other_other --> contact_help contact_help(((Contact the\nJunifer team))) missing_mask --> read_adding_mask_start read_adding_mask_start("Read Creating a Junifer extension") read_adding_mask_start --> read_adding_mask read_adding_mask("Read Adding Masks") read_adding_mask --> missing_other_solved missing_parcellation --> read_adding_parcellation_start read_adding_parcellation_start("Read Creating a Junifer extension") read_adding_parcellation_start --> read_adding_parcellation read_adding_parcellation("Read Adding Parcellations") read_adding_parcellation --> missing_other_solved missing_coordinates --> read_adding_coordinates_start read_adding_coordinates_start("Read Creating a Junifer extension") read_adding_coordinates_start --> read_adding_coordinates read_adding_coordinates("Read Adding Coordinates") read_adding_coordinates --> missing_other_solved missing_other_solved{Did you solve your issue?} missing_other_solved -->|Yes| read_using_final missing_other_solved -->|No| missing_other_contact missing_other_contact(Contact the\nJunifer team) missing_other_contact --> missing_other_issue missing_other_issue(((Submit a\nFEATURE REQUEST\nissue in Github))) read_using_final(Read Using Junifer) read_using_final --> final_yaml final_yaml(Create/edit the YAML file) final_yaml --> final_run final_run(Use junifer run to test your YAML configuration) final_run --> question_final_run_worked question_final_run_worked{"Did it work?"} question_final_run_worked -->|No| question_error_run question_error_run{"Is it an issue\nwith my YAML file?"} question_error_run -->|Yes| final_yaml question_error_run -->|No| error_contact error_contact(Contact the\nJunifer team) error_contact --> error_issue error_issue(((Submit a\nBUG REPORT issue\nin Github))) question_final_run_worked -->|Yes| final_queue final_queue(Use junifer queue to compute your features) final_queue --> final_magic final_magic(((Let junifer do its magic!))) click read_understanding href "https://juaml.github.io/junifer/main/understanding/index.html" click read_using href "https://juaml.github.io/junifer/main/using/index.html" click read_using_final href "https://juaml.github.io/junifer/main/using/index.html" click read_extending_datagrabber_start href "https://juaml.github.io/junifer/main/extending/extension.html" click read_extending_datagrabber href "https://juaml.github.io/junifer/main/extending/datagrabber.html" click read_extending_marker_start href "https://juaml.github.io/junifer/main/extending/extension.html" click read_extending_marker href "https://juaml.github.io/junifer/main/extending/marker.html" click read_adding_mask_start href "https://juaml.github.io/junifer/main/extending/extension.html" click read_adding_mask href "https://juaml.github.io/junifer/main/extending/masks.html" click read_adding_parcellation_start href "https://juaml.github.io/junifer/main/extending/extension.html" click read_adding_parcellation href "https://juaml.github.io/junifer/main/extending/parcellations.html" click read_adding_coordinates_start href "https://juaml.github.io/junifer/main/extending/extension.html" click read_adding_coordinates href "https://juaml.github.io/junifer/main/extending/coordinates.html" click error_issue href "https://github.com/juaml/junifer/issues/new/choose" _blank click missing_other_issue href "https://github.com/juaml/junifer/issues/new/choose" _blank click contribute_marker href "https://github.com/juaml/junifer/issues/new/choose" _blank click contribute_datagrabber href "https://github.com/juaml/junifer/issues/new/choose" _blank click error_contact href "https://juaml.github.io/junifer/main/help.html" click contact_help href "https://juaml.github.io/junifer/main/help.html" click missing_other_contact href "https://juaml.github.io/junifer/main/help.html"